Questions related to Structure Determination
This advance from the machine learning method AlphaFold totally stopped me in my tracks. To me it seems that many things will change in how we do research and what research we do. Many biological and medical questions can now be better addressed from the structural and mechanistic perspective. This seems likely to enable many rapid advances in things such as precision molecular medicine.
As noted in their Nature paper, accurate models will enable a wide range of applications: from homology search and putative function assignment to molecular replacement structure determinations and druggable pocket detection for the human proteome.
How do you imagine that we will harness this information of human protein folds for research and medicine?
I am currently working on a project on cryoEM single particle analysis of protein complexes. Though using HPLC size chromotography can separate the complexes and individual subunits, the structure is not homogeneous tested by negative staining. It might be due to the buffer used. However, how to choose the buffer? and how to access the stability of the protein complexes? Any suggestion is welcome.
I'm working in the field of plants, isolation, and structure determination of biologically active natural compounds.
I need NMR of proton, carbon-13, 2D,...
Any suggestions in this regard; free book, course, or support is valuable.
My question is about the Debye-Scherrer equation, which contains the constant K, according to my knowledge 0.9 is used for cubic structure, however, my sample has a hexagonal structure (determined by the XRD results), so I should look for the K value more appropriated for this structure.
I need to determine the open formula of our complex, presumably consisting of sodium tungstate Na2WO4 and aluminum sulfate Al2 (SO4) 3. Our problem is that with an increase in the concentration of the solution above 10 ^ -3 mol / l, the properties and possibly the structure change and it is impossible to achieve a stable monosalt for determining the structure. We need an exact formula to be determined inside the solution. I am waiting for your answers and terms of cooperation.
As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data.
However, in many cases (e.g. attached image), when you visualize the densities, there are negative (red) density blobs not containing any atoms inside. Just empty space inside. There is nothing in the model in those regions of space. How it should be interpreted?
Could you tell me please what I am missing?
Would be grateful for any help,
Please aid with software as well as strategies in order to get X-ray structure in a similar fashion to single crystal X-ray refinement. We have D2 Phaser-Bruker XRD instrument to obtain PXRD data available. Thanks in advance
The individual responds to the stimuli with the help of cognitive structures and experiences.
The quantity and quality of such knowledge structures determines the type and quantity of the response.
We need to modify, improve and develop knowledge structures.
In circular dichroism analysis, I have used k2d2 server for estimation of alpha helix and beta strand but how i can determine the qualities of such estimation by graphically or numerically using error interval.
I am going to study the occupations of Wyckoff sites for intermetallic compounds based on single crystals prepared under different conditions. I want to know which code, among Crystals, WingX, Shelx, etc. is the best for this purpose?
Thank you very much in advance.
To expand upon the question, I am currently studying a material for which I need to carry out an ISIF=3 relaxation. I keep ISYM=2, which is the default value, and the symmetry of the structure is determined a the beginning of the run to be C2, which is what I expect it to be. This is pretty low symmetry, but still a symmetry nonetheless. Over the course of the ISIF=3 relaxation, this symmetry is eventually broken, and subsequent ISIF=3 continuation runs tell me my structure is now at C1 symmetry instead. This is not the desired result.
Why is this happening? In my experience, VASP is pretty good about maintaining the symmetry as long as it is determined to be correct at the beginning. In the past, I've dealt with bulk wurtzite CdS and CdSe, which both have fairly high symmetry, and all ISIF=3 relaxations of those materials preserved the correct symmetry. But for some reason, my current C2 structure can't keep to that during relaxation.
Any help would be greatly appreciated.
ICSD and springer both are paid database. Is there any open access database for crystal structure determination?
Thanks in advance!
Hi, I was searching the polarity of Eicosapentaenoic acid and Docosahexaenoic acid and I found a site online that said most hydrocarbons were non-polar. Also I found some examples using Lewis structure to determine the polarity for simple structure of some compunds but not hydrocarbons.
Is there a set of rules to determine the polarity of icosapentaenoic acid and Docosahexaenoic acid?
I am currently working on reviving an XRD machine.it is SMART APEX II form bruker.
the x-ray source is Molybdenum.
The problem I am facing now is that the main application is protein x-ray crystallography.Is there a way to use the mo x-ray source with protein structure determination?
I am unfamiliar to how MALDI-TOF MS can identify protein structure. I have read websites indicating that it can be done. However, I would like to know of how accurate are the results of MALDI-TOF MS vs. Xray crystallography. Does anyone have references that I may read regarding use of MALDI-TOF MS for protein structure determination? Thanks in advance.
I am working with DNA-protein complex crystallization . I have tried fragments varying in length from 35 bp to 27 bp. DNA is specific in terms of affinity to protein. I am getting crystals with all the fragments but they are not diffracting . They form gelatinous like morphology when disturbed. How to improve for diffraction?
When FeCl2/FeCl3 is added to chalcones, a reddish-brown colour appears, however, the equations for this reaction reported in the literature always show the chalcone as a charge balancing ion, rather than a ligand coordinated to the metal centre. So, what type of interaction exists in this case between Fe and the chalcone? Is it ionic or a coordinate bond?
The unit cell of a magnetic structure is determined by the propagation vector. In my opinion, a propagation vector of (001) should give the same result of (000). But I find some reports mentioned that the propagation vector for their structures are (001) or (010) or (100). What is the difference between (000) and (001)?
I have prepared a nanocrystals which don't have reference data. I have collected the PXRD data for both bulk and the nanocrystal. In my manuscript, I have compare these two data. I want to know its crystal system.
I am writing a review paper on X-ray crystallography, I need help in following fields:
- Analysis of diffraction pattern,
- Electron density map,
- Structure determination and refinement.
I have sent my crystal for synchrotron and now I have diffraction images. I want to start the data processing. It is my first time and I need to know the step by step protocols (for MR or SeMet) and the needed software for each steps from diffraction images until pdb file submitting.
Can any university accept outside students doing attachment for 1 week and analysis on structure solution using TOPAS (Bruker software)?
We can discuss a fee later.
XRD Department, National University of Malaysia.
To be more specific, what kind of experiments would you perform to get structural constraints data for small, medium and large proteins? I am struggling to find a paper that solely talks about this without going to the details of each technique. I just want to know what the experiments does and what kind of information do you get for the experiment being done on different size of proteins. Any papers that you could suggest would be much appreciated! Thank you in advance
As commenters pointed out, I realised my questions are too broad. So I am talking about soluble proteins using solution state NMR technique.
My plan is to run a MD simulation, with the NMR derived constraints from the closed to the intermediate structure. However, not having a NMR background, I don't know how to convert Hydrogen exchange data into distance constraints.
I want to calculate secondary structure of the proteins by FTIR.
To do so I recorded the Primary spectra of my protein. In order to get more resolution of the peaks I am doing deconvolution followed by curve fitting of the primary spectra. In doing so I have found the following problems. I am using OPUS software provide by Brooker.
1. I do not understand how I can avoid over deconvolution of primary spectra. i.e. how to know the selected values for bandwidth and noise suppression factor are correct. Just by looking the spectra while deciding these values or is another statistical method is available which could tell the reliability of deconvoluted spectra?
2. I have selected amide 1 region for the secondary structure determination. (1700 cm-1 to 1600cm-1). The baseline was corrected only within this region and proceeded for deconvolution. While performing deconvolution I observe that some of the region of spectra, ma be from 1686 to 1670cm-1, were going to a more negative value than at 1700cm-1 which starts from zero. This is giving me problems while performing curve fitting.
For Curve fitting.
1. I determine the secondary derivative of my deconvoluted spectra and select the peak at particular wavenumber.
2. in the opus software one needs to give another two parameter
a. Intensity at particular wave number
I don't have a problem in selecting value for intensity, but which value should be put in the width column ?.
3. After doing curve fitting it will give the value of RMS. I know the meaning of RMS, but how can I know what is the acceptable limit for this value. After every fit it will give the RMS value which is always different. I came to know from the literature that RMS value should be low. But how low?
I want to know about the mosaicity in macromolecular crystallography as a novice. How does it impact the structure determination of the protein?
I have been reading up on the TGR5 receptor and how it could be used in treatment of various aspects of metabolic syndrome, however, a crystal structure has not yet been found and through my reading I cannot find why, so I was wondering if anybody knew and what studies could be done in order to solve it?
Distance information provides powerful insights for macromolecular structure determination and analysis. What are the promising, current and emerging approaches for this method?
I want to make the structural resolution of a condensed phosphate hydrate and I have the laboratory data as datafile.dat, I already started working with DICVOL and TREOR, and they give me the same thing parameters, but I have no idea about the corresponding isotype to start work with Fullprof, so I think i must work with FOX or Expo
I have cloned my domain in an expression vector and forgot to include stop codon at its 3' end and six more aminoacids were included from the vector.
If up to what no of residues from vector?
I am solving a structure of which I have X-ray data up to 1.5 A resolution. However, there are not so many spots in the highest resolution region, so that when I solve the structure (with a good model I have from a closely related protein) everything looks very good in terms of density fitting and stats, but the overall R and freeR factors are still quite high (0.23 and 0.26).
The only way I found to lower the R factors is to discard the higher res data. For instance, if I don't consider the data <1.9 my R factor decrease by 2-3%, and if I go down to 2.1 A my R factor goes below 0.20, but the density around my residues is not so good anymore. Any suggestion on what is best to do in this situation? Would you prefer solving a structure with lower R factors and lower resolution, or higher resolution but higher R factors?
In order to deposit a protein structure on the PDB database the file needs to have a TER card at the end of the chain.
In the past I have added them manually in the PDB file and changed the number of the atoms accordingly, but it is a pain and, particularly if the protein has more than 1 chain, very time consuming!
Do you know of any utilities that can add the TER cards and update the atom numbers automatically?